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Microorganisms, Volume 12, Issue 1 (January 2024) – 230 articles

Cover Story (view full-size image): Cancer treatment negatively affects gut homeostasis via a disrupted mucosal barrier, leading to bacterial translocation and a significant inflammatory immune response. The scientific and clinical communities have widely accepted the crucial role of the microbiome in tumor development. Moreover, mounting evidence described the impact of the microbiome composition on chemo- and immunotherapy efficacy and treatment-induced late toxicity. Gut microbiota modulation via probiotics and fecal microbiota transplantation represents an emerging trend for increasing bacterial diversity, preventing inflammatory processes, and improving response to cancer therapies while minimizing side effects. A deep understanding of the host–microbiome crosstalk will help to bring a microbiome-based approach to routine clinical practice. View this paper
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29 pages, 8331 KiB  
Review
Natural Killer Cells and Cytotoxic T Cells: Complementary Partners against Microorganisms and Cancer
by Aristo Vojdani, Sadi Koksoy, Elroy Vojdani, Mark Engelman, Carina Benzvi and Aaron Lerner
Microorganisms 2024, 12(1), 230; https://doi.org/10.3390/microorganisms12010230 - 22 Jan 2024
Viewed by 1973
Abstract
Natural killer (NK) cells and cytotoxic T (CD8+) cells are two of the most important types of immune cells in our body, protecting it from deadly invaders. While the NK cell is part of the innate immune system, the CD8+ [...] Read more.
Natural killer (NK) cells and cytotoxic T (CD8+) cells are two of the most important types of immune cells in our body, protecting it from deadly invaders. While the NK cell is part of the innate immune system, the CD8+ cell is one of the major components of adaptive immunity. Still, these two very different types of cells share the most important function of destroying pathogen-infected and tumorous cells by releasing cytotoxic granules that promote proteolytic cleavage of harmful cells, leading to apoptosis. In this review, we look not only at NK and CD8+ T cells but also pay particular attention to their different subpopulations, the immune defenders that include the CD56+CD16dim, CD56dimCD16+, CD57+, and CD57+CD16+ NK cells, the NKT, CD57+CD8+, and KIR+CD8+ T cells, and ILCs. We examine all these cells in relation to their role in the protection of the body against different microorganisms and cancer, with an emphasis on their mechanisms and their clinical importance. Overall, close collaboration between NK cells and CD8+ T cells may play an important role in immune function and disease pathogenesis. The knowledge of how these immune cells interact in defending the body against pathogens and cancers may help us find ways to optimize their defensive and healing capabilities with methods that can be clinically applied. Full article
(This article belongs to the Special Issue Latest Review Papers in Molecular Microbiology and Immunology 2023)
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15 pages, 3101 KiB  
Article
Comparison of Different Vascular Biomarkers for Predicting In-Hospital Mortality in Severe SARS-CoV-2 Infection
by Renáta Sütő, Marianna Pócsi, Miklós Fagyas, Edit Kalina, Zsolt Fejes, Zoltán Szentkereszty, János Kappelmayer and Béla Nagy Jr.
Microorganisms 2024, 12(1), 229; https://doi.org/10.3390/microorganisms12010229 - 22 Jan 2024
Cited by 1 | Viewed by 981
Abstract
Severe SARS-CoV-2 elicits a hyper-inflammatory response that results in intravascular inflammation with endothelial injury, which contributes to increased mortality in COVID-19. To predict the outcome of severe SARS-CoV-2 infection, we analyzed the baseline level of different biomarkers of vascular disorders in COVID-19 subjects [...] Read more.
Severe SARS-CoV-2 elicits a hyper-inflammatory response that results in intravascular inflammation with endothelial injury, which contributes to increased mortality in COVID-19. To predict the outcome of severe SARS-CoV-2 infection, we analyzed the baseline level of different biomarkers of vascular disorders in COVID-19 subjects upon intensive care unit (ICU) admission and prior to any vaccination. A total of 70 severe COVID-19 patients (37 survivors and 33 non-survivors) were included with 16 age- and sex-matched controls. Vascular dysfunction was monitored via soluble VCAM-1, E-selectin, ACE2 and Lp-PLA2, while abnormal platelet activation was evaluated by soluble P-selectin and CD40L in parallel. These results were correlated with routine laboratory parameters and disease outcomes. Among these parameters, VCAM-1 and ACE2 showed significantly higher serum levels in COVID-19 patients with early death vs. convalescent subjects. VCAM-1 was significantly correlated with the Horowitz index (r = 0.3115) and IL-6 (r = 0.4599), while ACE2 was related to E-selectin (r = 0.4143) and CD40L (r = 0.2948). Lp-PLA2 was altered in none of these COVID-19 subcohorts and showed no relationship with the other parameters. Finally, the pre-treatment level of VCAM-1 (≥1420 ng/mL) and ACE2 activity (≥45.2 μU/mL) predicted a larger risk for mortality (Log-Rank p = 0.0031 and p = 0.0117, respectively). Vascular dysfunction with endothelial cell activation is linked to lethal COVID-19, and highly elevated soluble VCAM-1 and ACE2 at admission to ICU may predict unfavorable outcomes. Full article
(This article belongs to the Special Issue Epidemiology of SARS-CoV-2/COVID-19 Infections)
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16 pages, 2258 KiB  
Article
Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants
by Kimberley Parkin, Debra J. Palmer, Valerie Verhasselt, Nelly Amenyogbe, Matthew N. Cooper, Claus T. Christophersen, Susan L. Prescott, Desiree Silva and David Martino
Microorganisms 2024, 12(1), 228; https://doi.org/10.3390/microorganisms12010228 - 22 Jan 2024
Viewed by 1402
Abstract
Complementary feeding induces dramatic ecological shifts in the infant gut microbiota toward more diverse compositions and functional metabolic capacities, with potential implications for immune and metabolic health. The aim of this study was to examine whether the age at which solid foods are [...] Read more.
Complementary feeding induces dramatic ecological shifts in the infant gut microbiota toward more diverse compositions and functional metabolic capacities, with potential implications for immune and metabolic health. The aim of this study was to examine whether the age at which solid foods are introduced differentially affects the microbiota in predominantly breastfed infants compared with predominantly formula-fed infants. We performed whole-genome shotgun metagenomic sequencing of infant stool samples from a cohort of six-month-old Australian infants enrolled in a nested study within the ORIGINS Project longitudinal birth cohort. Infants born preterm or those who had been administered antibiotics since birth were excluded. The taxonomic composition was highly variable among individuals at this age. Predominantly formula-fed infants exhibited a higher microbiome diversity than predominantly breastfed infants. Among the predominantly breastfed infants, the introduction of solid foods prior to five months of age was associated with higher alpha diversity than solid food introduction after six months of age, primarily due to the loss of Bifidobacterium infantis. In contrast, the age at which solid food was introduced was not associated with the overall change in diversity among predominantly formula-fed infants but was associated with compositional changes in Escherichia abundance. Examining the functional capacity of the microbiota in relation to these changes, we found that the introduction of solid foods after six months of age was associated with elevated one-carbon compound metabolic pathways in both breastfed and formula-fed infants, although the specific metabolic sub-pathways differed, likely reflecting different taxonomic compositions. Our findings suggest that the age of commencement of solid foods influences the gut microbiota composition differently in predominantly breastfed infants than in predominantly formula-fed infants. Full article
(This article belongs to the Special Issue Gut Microbiota: Metagenomics to Study Ecology)
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14 pages, 11615 KiB  
Article
miR-4687-5p Affects Intracellular Survival of Mycobacterium tuberculosis through Its Regulation of NRAMP1 Expression in A549 Cells
by Chaoqun Meng, Guangxin Chen, Yue Liu, Da Wen, Jia Cui, Li Dong, Zhiqiang Yang, Hangting Meng, Yuanting Gao, Jiao Feng, Xiaogang Cui and Changxin Wu
Microorganisms 2024, 12(1), 227; https://doi.org/10.3390/microorganisms12010227 - 22 Jan 2024
Viewed by 951
Abstract
Tuberculosis (TB), as one of the leading causes of death, poses a serious predicament to the world. MicroRNAs (miRNAs) play a role in the post-transcriptional regulation of gene expression. It has been reported that the expression of miRNAs changes upon mycobacterial infection; the [...] Read more.
Tuberculosis (TB), as one of the leading causes of death, poses a serious predicament to the world. MicroRNAs (miRNAs) play a role in the post-transcriptional regulation of gene expression. It has been reported that the expression of miRNAs changes upon mycobacterial infection; the screening and identification of miRNAs regulating the expression of genes could benefit our understanding of TB pathogenesis and generate effective strategies for its control and prevention. In this study, luciferase assays showed that miR-4687-5p is bound to the 3′-untranslated region of natural resistance-associated macrophage protein 1 (NRAMP1). Additionally, we found a significant increase in miR-4687-5p expression in Mycobacterium tuberculosis (Mtb)-infected A549 cells. Concomitantly, we detected a reduced level of NRAMP1 expression, suggesting that NRAMP1 is one of the targets of miR-4687-5p. Infection experiments evidenced that the transfection of miR-4687-5p induced a decrease in NRAMP1 expression and increased intracellular Mtb loads post-infection, indicating that miR-4687-5p promotes the intracellular survival of Mtb through its downregulation of the NRAMP1 protein level. We also found that the transfection of miR-4687-5p induced increased apoptosis and decreased cell proliferation post-infection with Mtb. The results presented in our study suggest that miR-4687-5p may be indicative of the susceptibility of Mtb infection to humans and could act as a potential therapeutic target for tuberculosis treatment. Full article
(This article belongs to the Special Issue Immunometabolism in Mycobacterium tuberculosis (M.tb) Infection)
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2 pages, 135 KiB  
Editorial
Highlighting New Perspectives on Musculoskeletal Infections
by Michele Fiore and Andrea Sambri
Microorganisms 2024, 12(1), 226; https://doi.org/10.3390/microorganisms12010226 - 22 Jan 2024
Viewed by 597
Abstract
The treatment of musculoskeletal and prosthetic joint infections represents a considerable challenge for patients, healthcare providers, and the healthcare system because of the high number of treatment failures and the significant economic burden [...] Full article
(This article belongs to the Special Issue Prosthetic and Bone Infections: A Multidisciplinary Approach)
12 pages, 1374 KiB  
Article
High Prevalence of Novel Sequence Types in Streptococcus pneumoniae That Caused Invasive Diseases in Kuwait in 2018
by Eiman Mokaddas, Mohammad Asadzadeh, Shabeera Syed and M. John Albert
Microorganisms 2024, 12(1), 225; https://doi.org/10.3390/microorganisms12010225 - 22 Jan 2024
Viewed by 969
Abstract
Background: Multilocus sequence typing (MLST) is used to gain insight into the population genetics of bacteria in the form of sequence type (ST). MLST has been used to study the evolution and spread of virulent clones of Streptococcus pneumoniae in many parts of [...] Read more.
Background: Multilocus sequence typing (MLST) is used to gain insight into the population genetics of bacteria in the form of sequence type (ST). MLST has been used to study the evolution and spread of virulent clones of Streptococcus pneumoniae in many parts of the world. Such data for S. pneumoniae are lacking for the countries of the Arabian Peninsula, including Kuwait. Methods: We determined the STs of all 31 strains of S. pneumoniae from invasive diseases received at a reference laboratory from various health centers in Kuwait during 2018 by MLST. The relationship among the isolates was determined by phylogenetic analysis. We also determined the serotypes by Quellung reaction, and antimicrobial susceptibility by Etest, against 15 antibiotics belonging to 10 classes. Results: There were 28 STs among the 31 isolates, of which 14 were new STs (45.2%) and 5 were rare STs (16.1%). Phylogenetic analysis revealed that 26 isolates (83.9%) were unrelated singletons, and the Kuwaiti isolates were related to those from neighboring countries whose information was gleaned from unpublished data available at the PubMLST website. Many of our isolates were resistant to penicillin, erythromycin, and azithromycin, and some were multidrug-resistant. Virulent serotype 8-ST53, and serotype 19A with new STs, were detected. Conclusions: Our study detected an unusually large number of novel STs, which may indicate that Kuwait provides a milieu for the evolution of novel STs. Novel STs may arise due to recombination and can result in capsular switching. This can impact the effect of vaccination programs on the burden of invasive pneumococcal disease. This first report from the Arabian Peninsula justifies the continuous monitoring of S. pneumoniae STs for the possible evolution of new virulent clones and capsular switching. Full article
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17 pages, 1823 KiB  
Article
Dupilumab Alters Both the Bacterial and Fungal Skin Microbiomes of Patients with Atopic Dermatitis
by Naoka Umemoto, Maki Kakurai, Takanao Matsumoto, Kenta Mizuno, Otomi Cho, Takashi Sugita and Toshio Demitsu
Microorganisms 2024, 12(1), 224; https://doi.org/10.3390/microorganisms12010224 - 22 Jan 2024
Viewed by 1481
Abstract
The skin microbiome at lesion sites in patients with atopic dermatitis (AD) is characterized by dysbiosis. Although the administration of dupilumab, an IL-4Rα inhibitor, improves dysbiosis in the bacterial microbiome, information regarding the fungal microbiome remains limited. This study administered dupilumab to 30 [...] Read more.
The skin microbiome at lesion sites in patients with atopic dermatitis (AD) is characterized by dysbiosis. Although the administration of dupilumab, an IL-4Rα inhibitor, improves dysbiosis in the bacterial microbiome, information regarding the fungal microbiome remains limited. This study administered dupilumab to 30 patients with moderate-to-severe AD and analyzed changes in both fungal and bacterial skin microbiomes over a 12-week period. Malassezia restricta and M. globosa dominated the fungal microbiome, whereas non-Malassezia yeast species increased in abundance, leading to greater microbial diversity. A qPCR analysis revealed a decrease in Malassezia colonization following administration, with a higher reduction rate observed where the pretreatment degree of colonization was higher. A correlation was found between the group classified by the Eczema Area and Severity Index, the group categorized by the concentration of Thymus and activation-regulated chemokine, and the degree of skin colonization by Malassezia. Furthermore, an analysis of the bacterial microbiome also confirmed a decrease in the degree of skin colonization by the exacerbating factor Staphylococcus aureus and an increase in the microbial diversity of the bacterial microbiome. Our study is the first to show that dupilumab changes the community structure of the bacterial microbiome and affects the fungal microbiome in patients with AD. Full article
(This article belongs to the Section Medical Microbiology)
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17 pages, 8395 KiB  
Article
Polyphasic Characterization of Brucella spp. in Livestock Slaughtered from Abattoirs in Eastern Cape, South Africa
by Koketso Desiree Mazwi, Francis Babaman Kolo, Ishmael Festus Jaja, Charles Byaruhanga, Ayesha Hassim and Henriette van Heerden
Microorganisms 2024, 12(1), 223; https://doi.org/10.3390/microorganisms12010223 - 22 Jan 2024
Viewed by 1148
Abstract
In livestock, brucellosis is mainly an asymptomatic disease except when abortion occurs; therefore, two serological tests are used for diagnosis as no single test is suitable. Abattoir samples enable a combination of culture, molecular, and serological tests to detect brucellosis. This study assessed [...] Read more.
In livestock, brucellosis is mainly an asymptomatic disease except when abortion occurs; therefore, two serological tests are used for diagnosis as no single test is suitable. Abattoir samples enable a combination of culture, molecular, and serological tests to detect brucellosis. This study assessed Brucella-specific PCR (ITS-PCR) to detect brucellosis and to conduct a molecular characterization of Brucella spp. isolated from PCR-positive livestock (n = 565) slaughtered at abattoirs and the appropriate sample tissue(s). ITS-PCR detected Brucella DNA in 33.6% of cattle, 14.5% of sheep, and 4.7% of pig tissues. Impure Brucella cultures from PCR-positive tissues were 43.6% (44/94) of cattle, 51.7% (15/29) of sheep, and 50% (2/4) of pigs with predominantly B. abortus identification with AMOS-PCR and low isolation of mixed B. abortus and B. melitensis in all species. In cattle, 33% of isolates were from lymph nodes, while in sheep 38.0% were from the liver and kidney and only from tonsils in pigs (2/4). Brucella infections identified with AMOS-PCR were present in seropositive and mainly seronegative (75.6–100%) livestock with the potential to cause brucellosis during pregnancy or breeding. This study demonstrated the value of the polyphasic approach, especially with chronic infections and the potential risk of these asymptomatic animals. Full article
(This article belongs to the Special Issue Advances in Brucella)
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19 pages, 1074 KiB  
Review
Helicobacter pylori: A Contemporary Perspective on Pathogenesis, Diagnosis and Treatment Strategies
by Asghar Ali and Khalid I. AlHussaini
Microorganisms 2024, 12(1), 222; https://doi.org/10.3390/microorganisms12010222 - 22 Jan 2024
Viewed by 3454
Abstract
Helicobacter pylori (H. pylori) is a Gram-negative bacterium that colonizes the gastric mucosa and is associated with various gastrointestinal disorders. H. pylori is a pervasive pathogen, infecting nearly 50% of the world’s population, and presents a substantial concern due to its [...] Read more.
Helicobacter pylori (H. pylori) is a Gram-negative bacterium that colonizes the gastric mucosa and is associated with various gastrointestinal disorders. H. pylori is a pervasive pathogen, infecting nearly 50% of the world’s population, and presents a substantial concern due to its link with gastric cancer, ranking as the third most common cause of global cancer-related mortality. This review article provides an updated and comprehensive overview of the current understanding of H. pylori infection, focusing on its pathogenesis, diagnosis, and treatment strategies. The intricate mechanisms underlying its pathogenesis, including the virulence factors and host interactions, are discussed in detail. The diagnostic methods, ranging from the traditional techniques to the advanced molecular approaches, are explored, highlighting their strengths and limitations. The evolving landscape of treatment strategies, including antibiotic regimens and emerging therapeutic approaches, is thoroughly examined. Through a critical synthesis of the recent research findings, this article offers valuable insights into the contemporary knowledge of Helicobacter pylori infection, guiding both clinicians and researchers toward effective management and future directions in combating this global health challenge. Full article
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9 pages, 1297 KiB  
Article
Gut Biogeography Accentuates Sex-Related Differences in the Murine Microbiome
by Melanie Ortiz-Alvarez de la Campa, Noelle Curtis-Joseph, Chapman Beekman and Peter Belenky
Microorganisms 2024, 12(1), 221; https://doi.org/10.3390/microorganisms12010221 - 22 Jan 2024
Viewed by 1510
Abstract
Recent studies have highlighted the influence of factors such as sex and sex-linked hormones on microbiome composition, raising concerns about the generalizability of findings. Here, we explore whether gut geography, specifically the upper and lower gastrointestinal tract (GI), contributes to sex-linked microbiome differences [...] Read more.
Recent studies have highlighted the influence of factors such as sex and sex-linked hormones on microbiome composition, raising concerns about the generalizability of findings. Here, we explore whether gut geography, specifically the upper and lower gastrointestinal tract (GI), contributes to sex-linked microbiome differences in mice. We collected microbial samples throughout the length of the GI from male and female C57B6/J mice at 6- and 8-weeks old, and conducted 16S rRNA sequencing. Our findings revealed significant sex-related differences, with Clostridium_sensu_stricto_1 more abundant in the male colon, while females exhibited higher levels of Dubosiella newyorkensis across all organs at 6 weeks. We also observed decreased Shannon alpha diversity in the small intestine compared to the lower GI, and this diversity decreased further at 8 weeks. Interestingly, our results suggest that age mitigates sex-related, but not gut geography-related differences in beta diversity, with implications for experimental outcomes and treatment strategies. This study underscores the dynamic nature of microbial diversity, influenced by sex, age, and GI localization, emphasizing the need for a more comprehensive understanding of microbiome dynamics in experimental research and clinical interventions. Full article
(This article belongs to the Section Gut Microbiota)
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10 pages, 418 KiB  
Article
Atopic Disease as a Risk Factor for Recurrent Herpetic Keratitis
by Margarita Safir and Michael Mimouni
Microorganisms 2024, 12(1), 220; https://doi.org/10.3390/microorganisms12010220 - 21 Jan 2024
Viewed by 844
Abstract
Recurrent herpetic keratitis is a leading cause of blindness worldwide. In this population-based cross-sectional study, the medical records of Israeli adolescents and young adults who underwent systematic preconscription evaluation for mandatory military service were reviewed. The prevalence of atopic conjunctival disease was evaluated [...] Read more.
Recurrent herpetic keratitis is a leading cause of blindness worldwide. In this population-based cross-sectional study, the medical records of Israeli adolescents and young adults who underwent systematic preconscription evaluation for mandatory military service were reviewed. The prevalence of atopic conjunctival disease was evaluated in cases with and without documented recurrent herpetic keratitis. The association was tested using uni- and multivariant analyses. Overall, 940,892 adolescents and young adults were included. The mean age was 17.57 ± 1.50 years (range 16–20 years), and 40.70% of participants were female. Recurrent herpetic keratitis was documented in 160 cases, with a prevalence of 0.017% in this age group. Compared to the general population, patients with recurrent herpetic keratitis were significantly more likely to be males (p = 0.003) with a concomitant diagnosis of atopic conjunctival disease (p < 0.0001). Patients with atopic conjunctival disease were 10.60-fold more likely to experience recurrent herpetic keratitis (95% confidence interval (CI): 6.76–16.64, p < 0.0001). Upon multivariate analysis, the results remained significant (p < 0.001). Cases of severe atopic conjunctival disease were more prone to recurrent HSV keratitis compared to mild cases (p < 0.001). These findings suggest that the timely appropriate treatment of atopic conjunctival disease may help reduce the frequency and severity of recurrent HSV keratitis and its complications. Full article
(This article belongs to the Special Issue Herpes Simplex Virus (HSV))
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27 pages, 1676 KiB  
Review
Megasphaera elsdenii: Its Role in Ruminant Nutrition and Its Potential Industrial Application for Organic Acid Biosynthesis
by Luciano da Silva Cabral and Paul J. Weimer
Microorganisms 2024, 12(1), 219; https://doi.org/10.3390/microorganisms12010219 - 21 Jan 2024
Cited by 2 | Viewed by 1598
Abstract
The Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although [...] Read more.
The Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of M. elsdenii usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). M. elsdenii has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of M. elsdenii to produce C2–C7 carboxylic acids—potential precursors for industrial fuel and chemical production—is examined. Full article
(This article belongs to the Section Veterinary Microbiology)
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6 pages, 211 KiB  
Communication
Novel Knowledge of Macrolide Resistance in Mycoplasma pneumoniae by Azithromycin Exposure
by Tomohiro Oishi, Nemu Hattori and Daisuke Yoshioka
Microorganisms 2024, 12(1), 218; https://doi.org/10.3390/microorganisms12010218 - 21 Jan 2024
Viewed by 933
Abstract
The rise of macrolide-resistant Mycoplasma pneumoniae (MRMP), marked by point mutations in the 23S rRNA gene, poses a growing global concern since its initial detection in 2001. The prominence of the A2063G mutation during this emergence remains unexplained. This study aimed to clarify [...] Read more.
The rise of macrolide-resistant Mycoplasma pneumoniae (MRMP), marked by point mutations in the 23S rRNA gene, poses a growing global concern since its initial detection in 2001. The prominence of the A2063G mutation during this emergence remains unexplained. This study aimed to clarify the possibility of detecting MRMP from recent clinical macrolide-susceptible M. pneumoniae through exposure to azithromycin (AZM), which has a long half-life and was launched immediately before the first MRMP detection. Six strains isolated from Japanese children in 2019 and reference strain (FH), all belonging to the recent dominant P1 genotype, two, or two subtype, were cultivated in a medium containing slightly higher concentrations than the originated minimum inhibitory concentration (MIC) of AZM and underwent sequencing if they grew. Four out of the seven strains grew after exposure to AZM, and C2617G and C2617A were detected, with no mutation in two strains. After another cultivation and sequencing, two of four strains grew, one was changed from C2617G to A2063G, and the other remained C2617A. The MIC of AZM in A2063G strains was 128 mg/mL; for C2617A, it was 0.0156 mg/mL. This is the first study to detect the strains with A2063G mutation from recent macrolide-susceptible M. pneumoniae using AZM exposure. Full article
13 pages, 1807 KiB  
Article
Skin Microbial Community Associated to Strawberry Disease in Farmed Rainbow Trout (Oncorhynchus mykiss Walbaum, 1792)
by Alda Pardo, Alejandro Villasante and Jaime Romero
Microorganisms 2024, 12(1), 217; https://doi.org/10.3390/microorganisms12010217 - 21 Jan 2024
Cited by 1 | Viewed by 1009
Abstract
Aquaculture plays a crucial role in addressing the growing global demand for food. However, diseases associated with intensive aquaculture practices, especially those affecting the skin, can present significant challenges to both fish health and the industry as a whole. Strawberry disease (SD), also [...] Read more.
Aquaculture plays a crucial role in addressing the growing global demand for food. However, diseases associated with intensive aquaculture practices, especially those affecting the skin, can present significant challenges to both fish health and the industry as a whole. Strawberry disease (SD), also known as red-mark syndrome, is a persistent and non-lethal skin condition observed in Rainbow Trout (Oncorhynchus mykiss) in the United States and various European countries. SD is a nonlethal skin condition of an unclear etiology that affects rainbow trout reared in freshwater close to the harvest period. We used a RNA-based approach to examine active microbiota in the SD skin lesions and compared to non-injured skin. Our results, based on using 16S rRNA gene next-generation sequencing, showed that the skin microbiota was dominated by the phyla Firmicutes, Proteobacteria, and Actinobacteria. The comparisons of the skin microbiota between injured and non-injured samples showed differences in the alpha diversity (Fisher index) and beta diversity metrics (ANOSIM). At the genus level, both Pseudomonas and Candidatus Midichloria were highlighted as the most abundant taxa detected in samples obtained from fish affected with strawberry diseases. In contrast, the most abundant taxa in non-injured skin were Escherichia-Shigella, Streptococcus, and Pseudoalteromonas. In conclusion, our study on SD revealed distinct differences in the microbiota composition between skin lesions and non-injured skin. This is the first description of microbiota associated with SD-injured skin samples using an RNA approach. Full article
(This article belongs to the Section Veterinary Microbiology)
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14 pages, 2027 KiB  
Article
Patterns of Spatial Variation in Rumen Microbiology, Histomorphology, and Fermentation Parameters in Tarim wapiti (Cervus elaphus yarkandensis)
by Jianzhi Huang, Yueyun Sheng, Pengfei Xue, Donghui Yu, Peng Guan, Jiangang Ren and Wenxi Qian
Microorganisms 2024, 12(1), 216; https://doi.org/10.3390/microorganisms12010216 - 20 Jan 2024
Viewed by 849
Abstract
The rumen is divided into multiple rumen sacs based on anatomical structure, and each has its unique physiological environment. Tarim wapiti preserved roughage tolerance after domestication, and adaptation to the desertified environment led to the development of a unique rumen shape and intraruminal [...] Read more.
The rumen is divided into multiple rumen sacs based on anatomical structure, and each has its unique physiological environment. Tarim wapiti preserved roughage tolerance after domestication, and adaptation to the desertified environment led to the development of a unique rumen shape and intraruminal environment. In this work, six Tarim wapiti were chosen and tested for fermentation parameters, microbes, and histomorphology in four rumen areas (Dorsal sac, DS; Ventral sac, VS; Caudodorsal blind sac, CDBS; Caudoventral blind sac, CVBS). Tarim wapiti’s rumen blind sac had better developed rumen histomorphology, the ventral sac was richer in VFAs, and the dominant bacteria varied most notably in the phylum Firmicutes, which was enriched in the caudoventral blind sac. The ventral sac biomarkers focused on carbohydrate fermentation-associated bacteria, the dorsal sac focused on N recycling, and the caudoventral blind sac identified the only phylum-level bacterium, Firmicutes; we were surprised to find a probiotic bacterium, Bacillus clausii, identified as a biomarker in the ventral sac. This research provides a better understanding of rumen fermentation parameters, microorganisms, and histomorphology in the Tarim wapiti rumen within a unique ecological habitat, laying the groundwork for future regulation targeting the rumen microbiota and subsequent animal production improvement. Full article
(This article belongs to the Section Gut Microbiota)
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16 pages, 4222 KiB  
Article
Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis
by Virginie Pilliol, Mamadou Beye, Laureline Terlier, Julien Balmelle, Idir Kacel, Romain Lan, Gérard Aboudharam, Ghiles Grine and Elodie Terrer
Microorganisms 2024, 12(1), 215; https://doi.org/10.3390/microorganisms12010215 - 20 Jan 2024
Viewed by 925
Abstract
Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter [...] Read more.
Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter piscolens (P. piscolens) in one case of severe periodontitis. Here, reporting on two additional necrotic pulp cases yielded the opportunity to characterise two co-cultivated M. massiliense isolates, both with P. piscolens, as non-motile, 1–2-µm-long and 0.6–0.8-µm-wide Gram-positive coccobacilli which were autofluorescent at 420 nm. The two whole genome sequences featured a 31.3% GC content, gapless 1,834,388-base-pair chromosome exhibiting an 85.9% coding ratio, encoding a formate dehydrogenase promoting M. massiliense growth without hydrogen in GG medium. These data pave the way to understanding a symbiotic, transkingdom association with P. piscolens and its role in oral pathologies. Full article
(This article belongs to the Section Medical Microbiology)
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15 pages, 735 KiB  
Article
Association of the Infant Gut Microbiome with Temperament at Nine Months of Age: A Michigan Cohort Study
by Tengfei Ma, Sihan Bu, Adannaya C. Nzerem, Nigel Paneth, Jean M. Kerver, Cybil Nicole Cavalieri and Sarah S. Comstock
Microorganisms 2024, 12(1), 214; https://doi.org/10.3390/microorganisms12010214 - 20 Jan 2024
Viewed by 1215
Abstract
Though studies in animals and humans link the gut microbiota to brain development and control of behavior, little research has examined this connection in healthy infants. This prospective study could determine associations between infant gut microbiota at 3 months, and infant temperament at [...] Read more.
Though studies in animals and humans link the gut microbiota to brain development and control of behavior, little research has examined this connection in healthy infants. This prospective study could determine associations between infant gut microbiota at 3 months, and infant temperament at 9 months, in a prospective pregnancy cohort (Michigan Archive for Research on Child Health; n = 159). Microbiota profiling with 16S rRNA gene sequencing was conducted on fecal samples obtained at 3 months of age. Based on the relative abundance of gut microbiotas, three groups were identified, and each group was characterized by different microbes. Infant temperament outcomes were reported by mothers using the Infant Behavior Questionnaire-Revised Very Short Form at a mean age of 9.4 months. Fully adjusted multivariate linear regression models showed that certain clusters were associated with higher negative emotionality scores, prominently among infants who had poor vitamin D intake. However, no associations were evident between gut microbiota clusters and temperament scales after FDR correction. After using three differential abundance tools, Firmicutes was associated with higher positive affect/surgency scores, whereas Clostridioides was associated with lower scores. An association between the gut microbiota and early infancy temperament was observed; thus, this study warrants replication, with a particular focus on vitamin D moderation. Full article
(This article belongs to the Special Issue Gut Microbiome and Children’s Health)
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16 pages, 1263 KiB  
Review
Hospital-Acquired Pneumonia and Ventilator-Associated Pneumonia: A Literature Review
by Mihnea Miron, Mihaela Blaj, Anca Irina Ristescu, Gabriel Iosep, Andrei-Nicolae Avădanei, Diana-Gabriela Iosep, Radu Crișan-Dabija, Alexandra Ciocan, Mihaela Perțea, Carmen Doina Manciuc, Ștefana Luca, Cristina Grigorescu and Mihaela Cătălina Luca
Microorganisms 2024, 12(1), 213; https://doi.org/10.3390/microorganisms12010213 - 20 Jan 2024
Viewed by 5981
Abstract
Hospital-acquired pneumonia (HAP) and its subtype, ventilator-associated pneumonia (VAP), remain two significant causes of morbidity and mortality worldwide, despite the better understanding of pathophysiological mechanisms, etiology, risk factors, preventive methods (bundle of care principles) and supportive care. Prior detection of the risk factors [...] Read more.
Hospital-acquired pneumonia (HAP) and its subtype, ventilator-associated pneumonia (VAP), remain two significant causes of morbidity and mortality worldwide, despite the better understanding of pathophysiological mechanisms, etiology, risk factors, preventive methods (bundle of care principles) and supportive care. Prior detection of the risk factors combined with a clear clinical judgement based on clinical scores and dosage of different inflammatory biomarkers (procalcitonin, soluble triggering receptor expressed on myelloid cells type 1, C-reactive protein, mid-regional pro-adrenomedullin, mid-regional pro-atrial natriuretic peptide) represent the cornerstones of a well-established management plan by improving patient’s outcome. This review article provides an overview of the newly approved terminology considering nosocomial pneumonia, as well as the risk factors, biomarkers, diagnostic methods and new treatment options that can guide the management of this spectrum of infections. Full article
(This article belongs to the Special Issue Overviews of Clinical Microbial Infection)
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12 pages, 913 KiB  
Article
Identification of Virulence Factors in Isolates of Candida haemulonii, Candida albicans and Clavispora lusitaniae with Low Susceptibility and Resistance to Fluconazole and Amphotericin B
by Letizia Angiolella, Florencia Rojas, Andrea Giammarino, Nicolò Bellucci and Gustavo Giusiano
Microorganisms 2024, 12(1), 212; https://doi.org/10.3390/microorganisms12010212 - 20 Jan 2024
Viewed by 1109
Abstract
Emerging life-threatening multidrug-resistant (MDR) species such as the C. haemulonii species complex, Clavispora lusitaniae (sin. C. lusitaniae), and other Candida species are considered as an increasing risk for human health in the near future. (1) Background: Many studies have emphasized that the [...] Read more.
Emerging life-threatening multidrug-resistant (MDR) species such as the C. haemulonii species complex, Clavispora lusitaniae (sin. C. lusitaniae), and other Candida species are considered as an increasing risk for human health in the near future. (1) Background: Many studies have emphasized that the increase in drug resistance can be associated with several virulence factors in Candida and its knowledge is also essential in developing new antifungal strategies. (2) Methods: Hydrophobicity, adherence, biofilm formation, lipase activity, resistance to osmotic stress, and virulence ‘in vivo’ on G. mellonella larvae were studied in isolates of C. haemulonii, C. albicans, and C. lusitaniae with low susceptibility and resistance to fluconazole and amphotericin B. (3) Results: Intra- and interspecies variability were observed. C. haemulonii showed high hydrophobicity and the ability to adhere to and form biofilm. C. lusitaniae was less hydrophobic, was biofilm-formation-strain-dependent, and did not show lipase activity. Larvae inoculated with C. albicans isolates displayed significantly higher mortality rates than those infected with C. haemulonii and C. lusitaniae. (4) Conclusions: The ability to adhere to and form biofilms associated with their hydrophobic capacity, to adapt to stress, and to infect within an in vivo model, observed in these non-wild-type Candida and Clavispora isolates, shows their marked virulence features. Since factors that define virulence are related to the development of the resistance of these fungi to the few antifungals available for clinical use, differences in the physiology of these cells must be considered to develop new antifungal therapies. Full article
(This article belongs to the Special Issue Fungal Infections and Antifungal Strategies)
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18 pages, 5660 KiB  
Article
Deconstructing the Dimensions of Mycobiome Fingerprints in Luohandu Cave, Guilin, Southern China
by Bai-Ying Man, Xing Xiang, Xiao-Yu Cheng, Hong-Mei Wang, Chun-Tian Su, Qi-Bo Huang, Yang Luo, Chao Zhang, Gang Cheng, Yu-Yang Ni and Xing-Hua Shao
Microorganisms 2024, 12(1), 211; https://doi.org/10.3390/microorganisms12010211 - 20 Jan 2024
Viewed by 733
Abstract
Subterranean karst caves are windows into the terrestrial subsurface to deconstruct the dimensions of mycobiome fingerprints. However, impeded by the constraints of remote locations, the inaccessibility of specimens and technical limitations, the mycobiome of subterranean karst caves has remained largely unknown. Weathered rock [...] Read more.
Subterranean karst caves are windows into the terrestrial subsurface to deconstruct the dimensions of mycobiome fingerprints. However, impeded by the constraints of remote locations, the inaccessibility of specimens and technical limitations, the mycobiome of subterranean karst caves has remained largely unknown. Weathered rock and sediment samples were collected from Luohandu cave (Guilin, Southern China) and subjected to Illumina Hiseq sequencing of ITS1 genes. A total of 267 known genera and 90 known orders in 15 phyla were revealed in the mycobiomes. Ascomycota dominated all samples, followed by Basidiomycota and Mortierellomycota. The sediments possessed the relatively highest alpha diversity and were significantly different from weathered rocks according to the diversity indices and richness metrics. Fifteen families and eight genera with significant differences were detected in the sediment samples. The Ca/Mg ratio appeared to significantly affect the structure of the mycobiome communities. Ascomycota appeared to exert a controlling influence on the mycobiome co-occurrence network of the sediments, while Ascomycota and Basidiomycota were found to be the main phyla in the mycobiome co-occurrence network of weathered rocks. Our results provide a more comprehensive dimension to the mycobiome fingerprints of Luohandu cave and a new window into the mycobiome communities and the ecology of subterranean karst cave ecosystems. Full article
(This article belongs to the Special Issue Genomics Approaches in Microbial Ecology)
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7 pages, 564 KiB  
Brief Report
Evaluation of a New Standardized Nasal Sampling Method for Detection of SARS-CoV-2 RNA via RT-PCR
by Johannes G. M. Koeleman, Sander Mol, Henk Brand and David S. Y. Ong
Microorganisms 2024, 12(1), 210; https://doi.org/10.3390/microorganisms12010210 - 20 Jan 2024
Viewed by 872
Abstract
The aim of this study was to compare the diagnostic accuracy of nasal sampling using a novel anterior nasal swab (ANS) (Rhinoswab) versus combined oro-nasopharyngeal (OP/NP) sampling in COVID-19 suspected patients. This prospective observational study was performed from 11 November to 2 December [...] Read more.
The aim of this study was to compare the diagnostic accuracy of nasal sampling using a novel anterior nasal swab (ANS) (Rhinoswab) versus combined oro-nasopharyngeal (OP/NP) sampling in COVID-19 suspected patients. This prospective observational study was performed from 11 November to 2 December 2021 (part 1), and from 16 January to 22 February 2022 (part 2). Adult patients who attended the emergency room with suspected COVID-19 were asked to participate. One ANS and one OP/NP sample were consecutively collected, and both were analyzed via reverse transcription polymerase chain reaction (RT-PCR). The result of the OP/NP sample was considered to be the reference standard. A total of 412 patients were included, of whom 171 (41.5%) had a positive RT-PCR of the OP/NP swab, whereas 139 (33.7%) were positive on the ANS sample. The overall diagnostic accuracy for ANS sampling in terms of sensitivity, specificity, positive predictive value, and negative predictive value was 80.7% (95% CI 73.8–86.2), 99.6% (95% CI 97.3–100), 99.3% (95% CI 95.5–100), and 87.9% (95% CI 83.3–91.4), respectively. In conclusion, ANS sampling with the Rhinoswab identified 80.7% of all presented COVID-19 patients in an emergency department. Future studies should investigate if nasal Rhinoswab self-sampling is suitable for reliable diagnosis of COVID-19 in an outpatient setting. Full article
(This article belongs to the Special Issue Diagnosis of Viral Infections 2.0)
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11 pages, 3366 KiB  
Case Report
Bartonella- and Borrelia-Related Disease Presenting as a Neurological Condition Revealing the Need for Better Diagnostics
by Marna E. Ericson, B. Robert Mozayeni, Laurie Radovsky and Lynne T. Bemis
Microorganisms 2024, 12(1), 209; https://doi.org/10.3390/microorganisms12010209 - 19 Jan 2024
Cited by 2 | Viewed by 3376
Abstract
The diagnostic tests available to identify vector-borne pathogens have major limitations. Clinicians must consider an assortment of often diverse symptoms to decide what pathogen or pathogens to suspect and test for. Even then, there are limitations to the currently available indirect detection methods, [...] Read more.
The diagnostic tests available to identify vector-borne pathogens have major limitations. Clinicians must consider an assortment of often diverse symptoms to decide what pathogen or pathogens to suspect and test for. Even then, there are limitations to the currently available indirect detection methods, such as serology, or direct detection methods such as molecular tests with or without culture enrichment. Bartonella spp., which are considered stealth pathogens, are particularly difficult to detect and diagnose. We present a case report of a patient who experienced a spider bite followed by myalgia, lymphadenopathy, and trouble sleeping. She did not test positive for Bartonella spp. through clinically available testing. Her symptoms progressed and she was told she needed a double hip replacement. Prior to the surgery, her blood was submitted for novel molecular testing, where Bartonella spp. was confirmed, and a spirochete was also detected. Additional testing using novel methods over a period of five years found Bartonella henselae and Borrelia burgdorferi in her blood. This patient’s case is an example of why new diagnostic methods for vector-borne pathogens are urgently needed and why new knowledge of the variable manifestations of Bartonellosis need to be provided to the medical community to inform and heighten their index of suspicion. Full article
(This article belongs to the Special Issue Bartonella and Bartonellosis: New Advances and Further Challenges)
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16 pages, 4875 KiB  
Article
A Novel Multi-Strain E3 Probiotic Formula Improved the Gastrointestinal Symptoms and Quality of Life in Chinese Psoriasis Patients
by Pui Ling Kella Siu, Chi Tung Choy, Helen Hoi Yin Chan, Ross Ka Kit Leung, Un Kei Chan, Junwei Zhou, Chi Ho Wong, Yuk Wai Lee, Ho Wang Chan, Claudia Jun Yi Lo, Joseph Chi Ching Tsui, Steven King Fan Loo and Stephen Kwok Wing Tsui
Microorganisms 2024, 12(1), 208; https://doi.org/10.3390/microorganisms12010208 - 19 Jan 2024
Viewed by 1102
Abstract
Psoriasis is a chronic immune-mediated inflammatory disease affecting the skin and other systems. Gastrointestinal disease was found to be correlated with psoriasis in previous studies and it can significantly affect the quality of life of psoriasis patients. Despite the importance of the gut [...] Read more.
Psoriasis is a chronic immune-mediated inflammatory disease affecting the skin and other systems. Gastrointestinal disease was found to be correlated with psoriasis in previous studies and it can significantly affect the quality of life of psoriasis patients. Despite the importance of the gut microbiome in gut and skin health having already been demonstrated in many research studies, the potential effect of probiotics on GI comorbidities in psoriasis patients is unclear. To investigate the effects of probiotics on functional GI comorbidities including irritable bowel syndrome, functional constipation, and functional diarrhea in psoriasis patients, we conducted a targeted 16S rRNA sequencing and comprehensive bioinformatic analysis among southern Chinese patients to compare the gut microbiome profiles of 45 psoriasis patients over an 8-week course of novel oral probiotics. All the participants were stratified into responders and non-responders according to their improvement in GI comorbidities, which were based on their Bristol Stool Form Scale (BSFS) scores after intervention. The Dermatological Life Quality Index (DLQI) score revealed a significant improvement in quality of life within the responder group (DLQI: mean 10.4 at week 0 vs. mean 15.9 at week 8, p = 0.0366). The proportion of psoriasis patients without GI comorbidity manifestation at week 8 was significantly higher than that at week 0 (week 0: Normal 53.33%, Constipation/Diarrhea 46.67%; week 8: Normal 75.56%, Constipation/Diarrhea 24.44%, p = 0.0467). In addition, a significant difference in the gut microbiome composition between the responders and non-responders was observed according to alpha and beta diversities. Differential abundance analysis revealed that the psoriasis patients exhibited (1) an elevated relative abundance of Lactobacillus acidophilus, Parabacteroides distasonis, and Ruminococcus bromii and (2) a reduced relative abundance of Oscillibacter, Bacteroides vulgatus, Escherichia sp., and Biophila wadsworthia after the 8-week intervention. The responders also exhibited a higher relative abundance of Fusicatenibacter saccharivorans when compared to the non-responders. In summary, our study discovers the potential clinical improvement effects of the novel probiotic formula in improving GI comorbidities and quality of life in psoriasis patients. We also revealed the different gut microbiome composition as well as the gut microbial signatures in the patients who responded to probiotics. These findings could provide insight into the use of probiotics in the management of psoriasis symptoms. Full article
(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease 2.0)
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19 pages, 2872 KiB  
Article
Potential Effects of Essential Oil from Plinia cauliflora (Mart.) Kausel on Leishmania: In Vivo, In Vitro, and In Silico Approaches
by Vanderlan N. Holanda, Thaíse G. S. Brito, João R. S. de Oliveira, Rebeca X. da Cunha, Ana P. S. da Silva, Welson V. da Silva, Tiago F. S. Araújo, Josean F. Tavares, Sócrates G. dos Santos, Regina C. B. Q. Figueiredo and Vera L. M. Lima
Microorganisms 2024, 12(1), 207; https://doi.org/10.3390/microorganisms12010207 - 19 Jan 2024
Viewed by 910
Abstract
In the search for new chemotherapeutic alternatives for cutaneous leishmaniasis (CL), essential oils are promising due to their diverse biological potential. In this study, we aimed to investigate the chemical composition and leishmanicidal and anti-inflammatory potential of the essential oil isolated from the [...] Read more.
In the search for new chemotherapeutic alternatives for cutaneous leishmaniasis (CL), essential oils are promising due to their diverse biological potential. In this study, we aimed to investigate the chemical composition and leishmanicidal and anti-inflammatory potential of the essential oil isolated from the leaves of Plinia cauliflora (PCEO). The chemical composition of PCEO showed β-cis-Caryophyllene (24.4%), epi-γ-Eudesmol (8%), 2-Naphthalenemethanol[decahydro-alpha] (8%), and trans-Calamenene (6.6%) as its major constituents. Our results showed that the PCEO has moderate cytotoxicity (CC50) of 137.4 and 143.7 μg/mL on mice peritoneal exudate cells (mPEC) and Vero cells, respectively. The PCEO was able to significantly decrease mPEC infection by Leishmania amazonensis and Leishmania braziliensis. The value of the inhibitory concentration (IC50) on amastigote forms was about 7.3 µg/mL (L. amazonensis) and 7.2 µg/mL (L. braziliensis). We showed that PCEO induced drastic ultrastructural changes in both species of Leishmania and had a high selectivity index (SI) > 18. The in silico ADMET analysis pointed out that PCEO can be used for the development of oral and/or topical formulation in the treatment of CL. In addition, we also demonstrated the in vivo anti-inflammatory effect, with a 95% reduction in paw edema and a decrease by at least 21.4% in migration immune cells in animals treated with 50 mg/kg of PCEO. Taken together, our results demonstrate that PCEO is a promising topical therapeutic agent against CL. Full article
(This article belongs to the Special Issue Research on Leishmania and Leishmaniasis)
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14 pages, 506 KiB  
Article
Metagenomic of Liver Tissue Identified at Least Two Genera of Totivirus-like Viruses in Molossus molossus Bats
by Roseane da Silva Couto, Endrya do Socorro Foro Ramos, Wandercleyson Uchôa Abreu, Luis Reginaldo Ribeiro Rodrigues, Luis Fernando Marinho, Vanessa dos Santos Morais, Fabiola Villanova, Ramendra Pati Pandey, Xutao Deng, Eric Delwart, Antonio Charlys da Costa and Elcio Leal
Microorganisms 2024, 12(1), 206; https://doi.org/10.3390/microorganisms12010206 - 19 Jan 2024
Viewed by 1031
Abstract
The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in [...] Read more.
The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack an envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between the Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses. Full article
(This article belongs to the Special Issue Advances in Viral Metagenomics)
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4 pages, 188 KiB  
Editorial
Diversity of Microorganisms and Their Metabolites in Food
by João Miguel Rocha, Biljana Kovacevik, Sanja Kostadinović Veličkovska, Mercedes Tamame and José António Teixeira
Microorganisms 2024, 12(1), 205; https://doi.org/10.3390/microorganisms12010205 - 19 Jan 2024
Viewed by 902
Abstract
Throughout history as well as the present, food microorganisms have been proven to play a significant role in human life [...] Full article
5 pages, 179 KiB  
Editorial
Editorial for the Special Issue: Environment Microorganisms and Their Enzymes with Biotechnological Application
by Myung-Ji Seo
Microorganisms 2024, 12(1), 204; https://doi.org/10.3390/microorganisms12010204 - 19 Jan 2024
Viewed by 1001
Abstract
The ubiquitous nature of microorganisms demonstrates their ability to survive and thrive in diverse ecological settings, and their presence in extreme environments that approach the known limits of adaptable living confers importance to their role in those ecosystems [...] Full article
12 pages, 4702 KiB  
Article
A Three-Dimensional Model of Bacterial Biofilms and Its Use in Antimicrobial Susceptibility Testing
by Hala R. Ali, Pamela Collier and Roger Bayston
Microorganisms 2024, 12(1), 203; https://doi.org/10.3390/microorganisms12010203 - 19 Jan 2024
Viewed by 1126
Abstract
(1) Background: The discrepant antimicrobial susceptibility between planktonic and biofilm bacterial modes poses a problem for clinical microbiology laboratories and necessitates a relevant 3D experimental model allowing bacteria to grow in biofilm mode, in vitro, for use in anti-biofilm susceptibility testing. (2) Methods: [...] Read more.
(1) Background: The discrepant antimicrobial susceptibility between planktonic and biofilm bacterial modes poses a problem for clinical microbiology laboratories and necessitates a relevant 3D experimental model allowing bacteria to grow in biofilm mode, in vitro, for use in anti-biofilm susceptibility testing. (2) Methods: This work develops a 3D biofilm model consisting of alginate beads containing S. aureus biofilm and encased within two thick layers of alginate matrix. The constructed model was placed on a thin Boyden chamber insert suspended on a 24-well culture plate containing the culture medium. The antibacterial activity of bacitracin and chlorhexidine digluconate (CD), either combined or separately, against 2D S. aureus culture was compared to that in the 3D biofilm model. Quantitative analysis and imaging analysis were performed by assessing the bacterial load within the matrix as well as measuring the optical density of the culture medium nourishing the matrix. (3) Results: The 3D biofilm model represented the typical complex characteristics of biofilm with greater insusceptibility to the tested antimicrobials than the 2D culture. Only bacitracin and CD in combination at 100× the concentration found to be successful against 2D culture were able to completely eliminate the 3D biofilm matrix. (4) Conclusions: The 3D biofilm model, designed to be more clinically relevant, exhibits higher antimicrobial insusceptibility than the 2D culture, demonstrating that the model might be useful for testing and discovering new antimicrobial therapies. The data also support the view that combination therapy might be the optimal approach to combat biofilm infections. Full article
(This article belongs to the Special Issue Advance Research on Bacterial Biofilm)
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14 pages, 2559 KiB  
Article
Comparative Evaluation of the Efficacy of Two Ectoparasiticides in Preventing the Acquisition of Borrelia burgdorferi by Ixodes scapularis and Ixodes ricinus: A Canine Ex Vivo Model
by Djamel Tahir, Virginie Geolier, Sophie Dupuis, Nouha Lekouch, Elisabeth Ferquel, Valérie Choumet and Marie Varloud
Microorganisms 2024, 12(1), 202; https://doi.org/10.3390/microorganisms12010202 - 18 Jan 2024
Viewed by 1078
Abstract
In dogs, tick infestation can cause damage ranging from a simple skin irritation to severe diseases and/or paralysis leading to animal death. For example, Ixodes ricinus and I. scapularis are among the tick species incriminated the most in the transmission of Borrelia burgdorferi [...] Read more.
In dogs, tick infestation can cause damage ranging from a simple skin irritation to severe diseases and/or paralysis leading to animal death. For example, Ixodes ricinus and I. scapularis are among the tick species incriminated the most in the transmission of Borrelia burgdorferi, the agent of human and canine Lyme borreliosis (LB). In this study, we aimed to compare the efficacy of two products designed for dogs—an oral systemic ectoparasiticide and a topical repellent ectoparasiticide—against the acquisition of B. burgdorferi by adult I. scapularis and I. ricinus using an ex vivo model. Thirty-two beagle dogs were included in a parallel-group-designed, randomized, single-center, negative-controlled efficacy study. The dogs were allocated to three groups based on gender and body weight: a fluralaner (F, Bravecto®) treatment group (n = 8), administered a single oral treatment on day 0 at the recommended dose; a dinotefuran–permethrin–pyriproxyfen (DPP, Vectra® 3D) treatment group (n = 8), topically treated on day 56 at the recommended dose; and an untreated control group (n = 16). Blood and hair were collected from each dog on days 58, 63, 70, 77, and 84. Hair was added to the silicone-based membrane separating two glass chambers forming the feeding unit (FU). Chamber 1 was filled with blood spiked with B. burgdorferi sensu stricto, strain B31 (105 cells/mL). Chamber 2, glued below chamber 1, was seeded with 20 adult I. scapularis or I. ricinus. The FUs (n = 240) were incubated at 37 °C with a humidity >90%. Tick survival, attachment, and feces presence were observed from 1 h up to 72 h after tick seeding. The uptake of B. burgdorferi was determined in ticks using nested polymerase chain reaction (nPCR). The acaricidal efficacy of DPP-treated hair was 100% within 1 h of tick release on every study day for both I. ricinus and I. scapularis. The speed of kill associated with DPP was sufficiently fast to prevent tick attachment and engorgement, and, consequently, to prevent the acquisition of B. burgdorferi. In the F-treated group, the acaricidal efficacy observed at 12 h, throughout the study, was <20% and <28% for I. scapularis and I. ricinus, respectively. Furthermore, tick feces were observed in the FUs, and several female ticks (I. scapularis (n = 55) and I. ricinus (n = 94)) tested positive for B. burgdorferi. The results provide proof of concept for the use of an ex vivo model based on an artificial feeding system to compare two ectoparasiticides against the acquisition of B. burgdorferi by I. ricinus and I. scapularis. In addition, our results demonstrate the superiority of DPP compared to F in the speed of acaricidal activity against ticks, as well as in preventing the acquisition of B. burgdorferi. Full article
(This article belongs to the Special Issue Ticks and Tick-Borne Diseases in Animals)
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18 pages, 4879 KiB  
Article
U2-Net and ResNet50-Based Automatic Pipeline for Bacterial Colony Counting
by Libo Cao, Liping Zeng, Yaoxuan Wang, Jiayi Cao, Ziyu Han, Yang Chen, Yuxi Wang, Guowei Zhong and Shanlei Qiao
Microorganisms 2024, 12(1), 201; https://doi.org/10.3390/microorganisms12010201 - 18 Jan 2024
Cited by 1 | Viewed by 1310
Abstract
In this paper, an automatic colony counting system based on an improved image preprocessing algorithm and convolutional neural network (CNN)-assisted automatic counting method was developed. Firstly, we assembled an LED backlighting illumination platform as an image capturing system to obtain photographs of laboratory [...] Read more.
In this paper, an automatic colony counting system based on an improved image preprocessing algorithm and convolutional neural network (CNN)-assisted automatic counting method was developed. Firstly, we assembled an LED backlighting illumination platform as an image capturing system to obtain photographs of laboratory cultures. Consequently, a dataset was introduced consisting of 390 photos of agar plate cultures, which included 8 microorganisms. Secondly, we implemented a new algorithm for image preprocessing based on light intensity correction, which facilitated clearer differentiation between colony and media areas. Thirdly, a U2-Net was used to predict the probability distribution of the edge of the Petri dish in images to locate region of interest (ROI), and then threshold segmentation was applied to separate it. This U2-Net achieved an F1 score of 99.5% and a mean absolute error (MAE) of 0.0033 on the validation set. Then, another U2-Net was used to separate the colony region within the ROI. This U2-Net achieved an F1 score of 96.5% and an MAE of 0.005 on the validation set. After that, the colony area was segmented into multiple components containing single or adhesive colonies. Finally, the colony components (CC) were innovatively rotated and the image crops were resized as the input (with 14,921 image crops in the training set and 4281 image crops in the validation set) for the ResNet50 network to automatically count the number of colonies. Our method achieved an overall recovery of 97.82% for colony counting and exhibited excellent performance in adhesion classification. To the best of our knowledge, the proposed “light intensity correction-based image preprocessing→U2-Net segmentation for Petri dish edge→U2-Net segmentation for colony region→ResNet50-based counting” scheme represents a new attempt and demonstrates a high degree of automation and accuracy in recognizing and counting single-colony and multi-colony targets. Full article
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